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For each of your scripts you have a GML file and YY file in the same directory (check via Explorer). You point the packer at the GML file (since that's where the code goes).

Using a script can be more convenient as it means that you don't have extra files in game [sub]directories.

This was a head scratcher. Looks like a GML file isn't created for a completely blank script, just the YY. Adding a single character to the script and saving the project created the GML file too.